Learning from microarray interlaboratory studies: Measures of precision for gene expression

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Duewer, David L ^a   Jones, Wendell D ^b   Reid, Laura H ^b   Salit, Marc ^c  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b Expression Analysis   (United States)

^c NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ACCURACY; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; LABORATORY TEST; MICROARRAY ANALYSIS; MOLECULAR PROBE; NONHUMAN; RAT; REFERENCE VALUE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; DIAGNOSIS, MEASUREMENT AND ANALYSIS; GENE EXPRESSION PROFILING; METHODOLOGY; STANDARD;

GENE EXPRESSION; GENE EXPRESSION PROFILING; LABORATORY TECHNIQUES AND PROCEDURES; MICROARRAY ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA;

EID: 65549108657     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-153     Document Type: Article

References (29)

1. Larkin JE Frank BC Gavras H Sultana R Quackenbush J Independence and reproducibility across microarray platforms Nat Methods 2005, 2:337-344. 10.1038/nmeth757 15846360
2. Irizarry RA Warren D Spencer F Kim IF Biswal S Frank BC Gabrielson E Garcia JGN Geoghegan J Germino G Griffin C Hilmer SC Hoffman E Jedlicka AE Kawasaki E Martinez-Murillo F Morsberger L Lee H Petersen D Quackenbush J Scott A Wilson M Yang YQ Ye SQ Yu W Multiple-laboratory comparison of microarray platforms Nat Methods 2005, 2:345-349. 10.1038/ nmeth756 15846361
3. MAQC Consortium The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotech 2006, 24:1151-1161. 10.1038/nbt1239
4. de Biève P Essential for metrology in chemistry, but not yet achieved: Truly internationally understood concepts and associated terms Metrologia 2008, 45:335-341. 10.1088/0026-1394/45/3/011
5. ISO ISO in brief. International Standards for a sustainable world. Geneva 2008. http://www.iso.org/iso/isoinbrief_2008.pdf
6. ISO ISO 5725-1:1994/Cor 1:1998 Accuracy (trueness and precision) of measurement methods and results. Part 1: General principles and definitions. Geneva 1994 http://www.iso.org/iso/iso_catalogue/ catalogue_tc/catalogue_detail.htm?csnumber=11833
7. JCGM 200-2008 International Vocabulary of Metrology - Basic and General Concepts and Associated Terms (VIM) Sèvres, France 3 2008 http://www.bipm.org/en/publications/guides/vim.html
8. ISO ISO 3534-1:2006 Statistics - Vocabulary and symbols - Part 1: General statistical terms and terms used in probability. Geneva 2006 http://www.iso.org/iso/iso_catalogue/catalogue_tc/ catalogue_detail.htm?csnumber=40145
9. ISO ISO/TR 22971:2005 Accuracy (trueness and precision) of measurement methods and results - Practical guidance for the use of ISO 5725-2:1994 in designing, implementing and statistically analysing interlaboratory repeatability and reproducibility results. Geneva 2005 http://www.iso.org/iso/iso_catalogue/catalogue_tc/ catalogue_detail.htm?csnumber=39780
10. Duewer DL Kline MC Sharpless KE Thomas JB Gary KT Sowell AL Micronutrients Measurement Quality Assurance Program: Helping participants use interlaboratory comparison exercise results to improve their long-term measurement performance Anal Chem 1999, 71:1870-1878. 10.1021/ac981074k 10330911
11. Pine PS Boedigheimer M Rosenzweig BA Turpaz Y He YD Delenstarr G Ganter B Jarnagin K Jones WD Reid LH Thompson KL Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples Pharmacogenomics 2008, 9:1753-63. 10.2217/14622416.9.11.1753 19018728
12. ISO ISO 5725-2:1994 Accuracy (trueness and precision) of measurement methods and results. Part 2: Basic method for the determination of repeatability and reproducibility of a standard measurement method. Geneva 1994 http://www.iso.org/iso/iso_catalogue/catalogue_tc/ catalogue_detail.htm?csnumber=11835
13. ISO ISO 5725-3:1994 Accuracy (trueness and precision) of measurement methods and results. Part 3: Intermediate measures of the precision of a standard measurement method. Geneva 1994 http://www.iso.org/iso/ iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=11834
14. Thompson M Wood R Using uncertainty functions to predict and specify the performance of analytical methods Accredit Qual Assur 2006, 10:471-478. 10.1007/s00769-005-0040-5
15. Holloway AJ Oshlack A Diyagama DS Bowtell DD Smyth GK Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis BMC Bioinformatics 2006, 7:511. 1664592 17118209 10.1186/1471-2105-7-511
16. Held GA Duggar K Stolovitzky G Comparison of Amersham and Agilent Microarray Technologies Through Quantitative Noise Analysis Omics 2006, 10:532-544. 10.1089/omi.2006.10.532 17233562
17. Affymetrix, Inc Statistical Algorithms Description Document Santa Clara, CA USA 2002 http://www.affymetrix.com/support/technical/whitepapers/ sadd_whitepaper.pdf
18. Mansourian R Mutch DM Antille N Aubert J Fogel P Le Goff JM Moulin J Petrov A Rytz A Voegel JJ Roberts MA The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data Bioinformatics 2004, 20:2726-2737. 10.1093/bioinformatics/bth319 15145801
19. Zhou L Rocke DM An expression index for Affymetrix GeneChips based on the generalized logarithm Bioinformatics 2005, 21:3983-3989. 10.1093/ bioinformatics/bti665 16159924
20. Liggett W Normalization and technical variation in gene expression measurements J Res Natl Inst Stand Technol 2006, 111:361-372. http://nvl.nist.gov/pub/nistpubs/jres/111/5/V111.N05.A02.pdf
21. Huber W von Heydebreck A Sültmann H Poustka A Vingron M Variance stabilization applied to microarray data calibration and to the quantification of differential expression Bioinformatics 2002, 18:S96-S104. 12169536
22. Weng L Dai H Zhan Y He Y Stepaniants SB Bassett DE Rosetta error model for gene expression analysis Bioinformatics 2006, 22(9):1111-1121. 10.1093/bioinformatics/btl045 16522673
23. Satterfield MB Lippa K Lu JL Salit M Microarray scanner performance over a 5-week period as measured with Cy3 and Cy5 serial dilution dye slides J Res Natl Inst Stand Technol 2008, 113:157-174. http://nvl.nist.gov/pub/ nistpubs/jres/113/3/V113.N03.A03.pdf
24. Thompson KL Rosenzweig BA Pine PS Retief J Turpaz Y Afshari CA Hamadeh HK Damore MA Boedigheimer M Blomme E Ciurlionis R Waring JF Fuscoe JC Paules R Tucker CJ Fare T Coffey EM He Y Collins PJ Jarnagin K Fujimoto S Ganter B Kiser G Kaysser-Kranich T Sina J Sistare FD Use of a mixed tissue RNA design for performance assessments on multiple microarray formats Nucleic Acids Res 2005, 33:e187. 1322274 16377776 10.1093/nar/ gni186
25. Eberwine J Yeh H Miyashiro K Cao Y Nair S Finnell R Zettel M Coleman P Analysis of gene expression in single live neurons Proc Natl Acad Sci U S A. 1992, 89(7):3010-3014. 10.1073/pnas.89.7.3010 1557406 48793
26. Pavese F Filipe E Some metrological considerations about replicated measurements on standards Metrologia 2006, 43:419-425. 10.1088/0026-1394/ 43/5/013
27. Duewer DL Kline MC Sharpless KE Thomas JB Stacewicz-Sapuntzakis M Sowell AL NIST Micronutrients Measurement Quality Assurance Program: Characterizing individual participant measurement performance over time Anal Chem 2000, 72:3611-3619. 10.1021/ac991481b 10952550
28. Duewer DL Kline MC Sharpless KE Thomas JB NIST Micronutrients Measurement Quality Assurance Program: Characterizing the measurement community's performance over time Anal Chem 2000, 72:4163-4170. 10.1021/ ac991480j 10994979
29. ISO ISO 5725-5:1998 Accuracy (trueness and precision) of measurement methods and results. Part 5: Alternative method for the determination of the precision of a standard measurement method. Geneva 1998 http://www.iso.org/iso/iso_catalogue/catalogue_tc/ catalogue_detail.htm?csnumber=1384